Complete Chloroplast Genome of Cnidium monnieri (Apiaceae) and Comparisons with Other Tribe Selineae Species

Ren, Tao; Aou, Xueyimu; Tian, Rongming; Li, Zhenbing; Peng, Chang; He, Xing‐Jin

doi:10.3390/d14050323

Cited by 18 publications

(31 citation statements)

References 79 publications

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“…It exists in all species’s genomes and is influenced by many factors, such as mutation pressure, natural selection, gene composition and gene length [ 55 ]. In the present study, all codons with RSCU > 1.00 were strongly biased towards A/U at the third codon position in seventeen Sanicula plastomes, which was consistent with the observation in most angiosperms [ 56 ], as well as in Apiaceae [ 30 – 32 , 35 – 39 ]. Perhaps the high AT content in plastome is the major reason for the bias towards A/U for codons ending in A/U [ 39 ].…”

Section: Discussionsupporting

confidence: 92%

“…In the present study, all codons with RSCU > 1.00 were strongly biased towards A/U at the third codon position in seventeen Sanicula plastomes, which was consistent with the observation in most angiosperms [ 56 ], as well as in Apiaceae [ 30 – 32 , 35 – 39 ]. Perhaps the high AT content in plastome is the major reason for the bias towards A/U for codons ending in A/U [ 39 ]. Leucine was the most abundant amino acid and was encoded by the highest number of codons, while cysteine was the rarest amino acid, as in most Apiaceae species [ 30 – 32 ].…”

Section: Discussionsupporting

confidence: 92%

“…Codons provide a link between nucleic acids and proteins, conveying genetic information [ 39 ]. The patterns of codon usage show basic characteristics of molecular evolution [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

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Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

Song,

Liu,

Zhao

et al. 2024

BMC Plant Biol

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Background The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution. Results In the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074–86,197 bp), a small single copy region (SSC: 17,047–17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176–26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33–52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68–25.28 Ma). Conclusion The plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 92%

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Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

Song,

Liu,

Zhao

et al. 2024

BMC Plant Biol

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“…Seven genes ( atpI , ccsA , cemA , matK , ndhA , petA , and rpoC1 ) were under positive selection in genus Stemona . The positive selection gene matK has been widely reported in other land plants, such as Paphiopedilum [ 58 ], Chrysosplenium [ 59 ], and tribe Selineae species [ 60 ]. The genes atpI , ndhA , and petA were related to photosynthesis; prior research has implied that light plays an important role in gene mutation rates, and these positive selection genes might be associated with sunlight conditions [ 59 ].…”

Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications

Wei

Li²

2022

Genes

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Stemona parviflora is an endangered species, narrowly endemic to Hainan and Southwest Guangdong. The taxonomic classification of S. parviflora remains controversial. Moreover, studying endangered species is helpful for current management and conservation. In this study, the first complete chloroplast genome of S. parviflora was assembled and compared with other Stemona species. The chloroplast genome size of S. parviflora was 154,552 bp, consisting of 87 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and one pseudogene. The ψycf1 gene was lost in the cp genome of S. sessilifolia, but it was detected in four other species of Stemona. The inverted repeats (IR) regions have a relatively lower length variation compared with the large single copy (LSC) and small single copy (SSC) regions. Long repeat sequences and simple sequence repeat (SSR) were detected, and most SSR were distributed in the LSC region. Codon usage bias analyses revealed that the RSCU value of the genus Stemona has almost no difference. As with most angiosperm chloroplast genomes, protein-coding regions were more conservative than the inter-gene spacer. Seven genes (atpI, ccsA, cemA, matK, ndhA, petA, and rpoC1) were detected under positive selection in different Stemona species, which may result from adaptive evolution to different habitats. Phylogenetic analyses show the Stemona cluster in two main groups; S. parviflora were closest to S. tuberosa. A highly suitable region of S. parviflora was simulated by Maxent in this study; it is worth noting that the whole territory of Taiwan has changed to a low fitness area and below in the 2050 s, which may not be suitable for the introduction and cultivation of S. parviflora. In addition, limited by the dispersal capacity of S. parviflora, it is necessary to carry out artificial grafts to expand the survival areas of S. parviflora. Our results provide valuable information on characteristics of the chloroplast genome, phylogenetic relationships, and potential distribution range of the endangered species S. parviflora.

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“…Currently, the molecular phylogenetic study of Cocconeiopsis is lacking and its exact phylogenetic position remains unknown. The chloroplast and mitochondrial genome are now widely used for phylogenomic and molecular evolutionary studies due to their conserved nature and relatively high substitution rate [5][6][7]. Kowallik et al [8] sequenced the chloroplast of a marine centric diatom, Odontella sinensis, providing the first organelle genome of a diatom.…”

Section: Introductionmentioning

confidence: 99%

Phylogeny and Evolution of Cocconeiopsis (Cocconeidaceae) as Revealed by Complete Chloroplast and Mitochondrial Genomes

Du,

Li,

2023

IJMS

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The genus Cocconeiopsis was separated from Navicula, but its systematic position is in debate. We sequenced the complete chloroplast and mitochondrial genome of Cocconeidaceae for the first time with Cocconeiopsis kantsiensis and investigated its phylogeny and evolutionary history. Results showed that the plastid genome was 140,415 bp long with 167 genes. The mitochondrial genome was 43,732 bp long with 66 genes. Comparative analysis showed that the plastid genome structure of C. kantsiensis was most similar to those of three Navicula species and Halamphora americana, and its size was significantly smaller than that of a monoraphid species. Its mitochondrial genome was similar to that of related species except for Phaeodactylum tricornutum. The multigene phylogeny reconstruction showed that Cocconeiopsis was sister to Didymosphenia but distant from Naviculaceae. The two-gene phylogenetic analysis containing 255 species showed Cocconeiopsis was sister to Cocconeis, and distant from Naviculaceae as well. Divergence time estimation indicates the common ancestor of cocconeid species occurred about 62.8 Ma and Cocconeiopsis diverged with monoraphid Cocconeis about 58.9 Ma. Our results support the assignment of Cocconeiopsis to Cocconeidaceae and that monoraphid cocconeids were likely evolved from the lineage of Cocconeiopsis.

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Complete Chloroplast Genome of Cnidium monnieri (Apiaceae) and Comparisons with Other Tribe Selineae Species

Cited by 18 publications

References 79 publications

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications

Phylogeny and Evolution of Cocconeiopsis (Cocconeidaceae) as Revealed by Complete Chloroplast and Mitochondrial Genomes

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